Hypothesistest for
each contrast
pe <- msqrob2::msqrob(object = pe, i = "ptmRel", formula = ~condition*subset, robust=TRUE, overwrite = T)
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
## Warning in rlm.default(X, y, method = "M", maxit = maxitRob): 'rlm' failed to
## converge in 1 steps
rowData(pe[["ptmRel"]])$msqrobModels[[2]] %>%
getCoef
## (Intercept) conditionA subsety conditionA:subsety
## -0.20364594 0.02035259 -0.03977042 0.02892887
contrasts <- c("conditionA", "conditionA + conditionA:subsety", "conditionA:subsety", "conditionA + 0.5 * conditionA:subsety", "conditionA + 0.6666667 * conditionA:subsety")
L <- makeContrast(c("conditionA = 0",
"conditionA + conditionA:subsety = 0",
"conditionA:subsety = 0",
"conditionA + 0.5 * conditionA:subsety = 0",
"conditionA + 0.6666667 * conditionA:subsety = 0"),
parameterNames = rowData(pe[["ptmRel"]])$msqrobModels[[2]] %>%
getCoef %>%
names)
pe <- hypothesisTest(object = pe, i = "ptmRel", contrast = L, overwrite = T)
Volcanoplot
volcanos <- list()
for (contrast in contrasts){
library(plotly)
volcanos[[contrast]] <-
rowData(pe[["ptmRel"]])[[contrast]]%>%
ggplot(aes(x = logFC, y = -log10(pval),
color = adjPval < 0.05,
annotation=rowData(pe[["ptmRel"]])[,3])) +
geom_point(cex = 2.5) +
scale_color_manual(values = alpha(c("black", "red"), 0.5)) + theme_minimal() +
ylab("-log10(pvalue)") +
ggtitle(contrast)
}
volcanos
## $conditionA
## Warning: Removed 68 rows containing missing values (geom_point).

##
## $`conditionA + conditionA:subsety`
## Warning: Removed 68 rows containing missing values (geom_point).

##
## $`conditionA:subsety`
## Warning: Removed 68 rows containing missing values (geom_point).

##
## $`conditionA + 0.5 * conditionA:subsety`
## Warning: Removed 68 rows containing missing values (geom_point).

##
## $`conditionA + 0.6666667 * conditionA:subsety`
## Warning: Removed 68 rows containing missing values (geom_point).

Heatmap
We first select the names of the ptms that were declared
signficant.
Significant ptms
for each contrast
tables <- list()
for (contrast in contrasts){
sigTable <- rowData(pe[["ptmRel"]])[[contrast]]
if(nrow(sigTable %>%
na.exclude %>%
filter(adjPval<0.05)) > 0){
sigTable <- sigTable %>%
na.exclude %>%
filter(adjPval<0.05) %>%
arrange(pval) %>%
mutate(
se = format(se, digits = 2),
df = format(df, digits =2),
t = format(t, digits = 2),
adjPval = format(adjPval, digits = 3),
rank = 1:length(logFC)
)
sigTable_print <- sigTable %>% mutate(peptidoform = rownames(sigTable)) %>% gt() %>% tab_header(title = md(contrast))
tables[[contrast]] <- sigTable
}
}
knitr::kable(tables)
| sp|P01019|ANGT_HUMAN (Oxidation (M)) 105 |
-3.2887952 |
0.16 |
4.8 |
-20.8 |
0.0000068 |
0.00193 |
1 |
| sp|P10909|CLUS_HUMAN (Phospho (STY)) 210 |
-1.6735301 |
0.33 |
32.9 |
-5.1 |
0.0000128 |
0.00193 |
2 |
| sp|P10451|OSTP_HUMAN (Oxidation (M)) 284 |
-0.7650361 |
0.17 |
82.4 |
-4.6 |
0.0000144 |
0.00193 |
3 |
| sp|P02765|FETUA_HUMAN (Oxidation (M)) 321 |
-1.2172094 |
0.29 |
68.9 |
-4.1 |
0.0000962 |
0.00969 |
4 |
| sp|O94769|ECM2_HUMAN (Oxidation (M)) 76 |
-0.6949871 |
0.18 |
73.2 |
-3.9 |
0.0001927 |
0.01366 |
5 |
| sp|P05060|SCG1_HUMAN (Phospho (STY)) 317 |
-0.8350259 |
0.21 |
62.4 |
-3.9 |
0.0002034 |
0.01366 |
6 |
| sp|O94769|ECM2_HUMAN (Phospho (STY)) 75 |
-0.7307004 |
0.19 |
80.5 |
-3.8 |
0.0002810 |
0.01607 |
7 |
| sp|P05060|SCG1_HUMAN (Phospho (STY)) 311 |
-0.7705091 |
0.20 |
81.8 |
-3.8 |
0.0003190 |
0.01607 |
8 |
| sp|P62328|TYB4_HUMAN (Acetyl (Protein N-term)) 1 |
0.8411341 |
0.18 |
13.0 |
4.8 |
0.0003640 |
0.01630 |
9 |
| sp|O94769|ECM2_HUMAN (Phospho (STY)) 245 |
0.4363289 |
0.12 |
68.0 |
3.6 |
0.0005450 |
0.02155 |
10 |
| sp|P01042|KNG1_HUMAN (Phospho (STY)) 275 |
-1.3223296 |
0.35 |
33.2 |
-3.8 |
0.0005882 |
0.02155 |
11 |
| sp|P10451|OSTP_HUMAN (Phospho (STY)) 280 |
-1.0756663 |
0.31 |
84.1 |
-3.5 |
0.0006994 |
0.02349 |
12 |
|
| sp|P10909|CLUS_HUMAN (Phospho (STY)) 210 |
-2.363970 |
0.52 |
32.9 |
-4.6 |
0.0000680 |
0.021 |
1 |
| sp|P01019|ANGT_HUMAN (Oxidation (M)) 105 |
-2.440847 |
0.21 |
4.8 |
-11.7 |
0.0001041 |
0.021 |
2 |
|
| sp|P01019|ANGT_HUMAN (Oxidation (M)) 105 |
-2.0683715 |
0.10 |
4.8 |
-19.8 |
0.0000086 |
0.00349 |
1 |
| sp|O94769|ECM2_HUMAN (Oxidation (M)) 76 |
-0.6015157 |
0.16 |
73.2 |
-3.9 |
0.0002451 |
0.03315 |
2 |
| sp|P07197|NFM_HUMAN (Phospho (STY)) 736 |
-1.4251552 |
0.33 |
23.6 |
-4.3 |
0.0002739 |
0.03315 |
3 |
| sp|Q14515|SPRL1_HUMAN (Oxidation (M)) 276 |
-1.5631381 |
0.38 |
29.1 |
-4.1 |
0.0003290 |
0.03315 |
4 |
|
| sp|P01019|ANGT_HUMAN (Oxidation (M)) 105 |
-2.4751795 |
0.11 |
4.8 |
-21.6 |
0.0000058 |
0.00232 |
1 |
| sp|O94769|ECM2_HUMAN (Oxidation (M)) 76 |
-0.6326728 |
0.15 |
73.2 |
-4.3 |
0.0000450 |
0.00906 |
2 |
| sp|P07197|NFM_HUMAN (Phospho (STY)) 736 |
-1.4166206 |
0.32 |
23.6 |
-4.4 |
0.0001969 |
0.02640 |
3 |
| sp|P10451|OSTP_HUMAN (Oxidation (M)) 284 |
-0.5165387 |
0.14 |
82.4 |
-3.8 |
0.0002620 |
0.02640 |
4 |
| sp|Q14515|SPRL1_HUMAN (Oxidation (M)) 276 |
-1.4812379 |
0.38 |
29.1 |
-3.9 |
0.0005106 |
0.03572 |
5 |
| sp|O94769|ECM2_HUMAN (Phospho (STY)) 75 |
-0.5560719 |
0.16 |
80.5 |
-3.6 |
0.0006166 |
0.03572 |
6 |
| sp|P02765|FETUA_HUMAN (Oxidation (M)) 321 |
-0.8730036 |
0.24 |
68.9 |
-3.6 |
0.0006205 |
0.03572 |
7 |
| sp|P01042|KNG1_HUMAN (Phospho (STY)) 275 |
-1.0204569 |
0.28 |
33.2 |
-3.7 |
0.0008739 |
0.04240 |
8 |
| sp|P05060|SCG1_HUMAN (Phospho (STY)) 311 |
-0.5699020 |
0.17 |
81.8 |
-3.4 |
0.0009469 |
0.04240 |
9 |
|
a = "sp|Q16610|ECM1_HUMAN (Phospho (STY)) 80"
b = "sp|P13611|CSPG2_HUMAN (Phospho (STY)) 2115"
tables <- list()
for (contrast in contrasts){
sigTable <- rowData(pe[["ptmRel"]])[[contrast]]
tables[[contrast]] <- sigTable %>% rownames_to_column("ptm") %>% filter(ptm==a|ptm==b)
}
knitr::kable(tables)
| sp|P13611|CSPG2_HUMAN (Phospho (STY)) 2115 |
NA |
NA |
NA |
NA |
NA |
NA |
| sp|Q16610|ECM1_HUMAN (Phospho (STY)) 80 |
-0.2646351 |
0.1593109 |
29.40381 |
-1.661124 |
0.1073162 |
0.9935778 |
|
| sp|P13611|CSPG2_HUMAN (Phospho (STY)) 2115 |
NA |
NA |
NA |
NA |
NA |
NA |
| sp|Q16610|ECM1_HUMAN (Phospho (STY)) 80 |
-0.0540587 |
0.1428702 |
29.40381 |
-0.3783766 |
0.707869 |
0.9965335 |
|
| sp|P13611|CSPG2_HUMAN (Phospho (STY)) 2115 |
NA |
NA |
NA |
NA |
NA |
NA |
| sp|Q16610|ECM1_HUMAN (Phospho (STY)) 80 |
0.2105764 |
0.2139903 |
29.40381 |
0.9840464 |
0.3331211 |
0.9521619 |
|
| sp|P13611|CSPG2_HUMAN (Phospho (STY)) 2115 |
NA |
NA |
NA |
NA |
NA |
NA |
| sp|Q16610|ECM1_HUMAN (Phospho (STY)) 80 |
-0.1593469 |
0.1069951 |
29.40381 |
-1.489291 |
0.1470595 |
0.7317265 |
|
| sp|P13611|CSPG2_HUMAN (Phospho (STY)) 2115 |
NA |
NA |
NA |
NA |
NA |
NA |
| sp|Q16610|ECM1_HUMAN (Phospho (STY)) 80 |
-0.1242508 |
0.1090502 |
29.40381 |
-1.139391 |
0.2637373 |
0.7749193 |
|